The present invention belongs to the technical field of unconventional oil and gas development, and relates to a method for calculating apparent permeability of porous media of shale reservoir. The method includes the steps of: S1, collecting basic parameters of shale gas reservoir, calculating to obtain a Knudsen coefficient and a contribution coefficient; S2, utilizing the Knudsen coefficient tojudge the flow state of the gas in the capillary tube, and establishing the corresponding gas mass transport equation; S3, according to the water saturation of the reservoir rock sample, determiningthe effective flow radius corresponding to the capillaries of different sizes; S4, establishing unified mass transport equation of gas in different flow states in capillary tubes; S5. according to theunified mass transport equation, calculating the apparent permeability of the capillary tube, and superposing the apparent permeabilities of the capillary tubes with different sizes to obtain the apparent permeability of the whole shale core. The method of the invention takes into account the influence of different capillary sizes, distribution frequencies and water saturation of shale, and the method provided by the invention is closer to the real situation of the reservoir and obtains more accurate data.